|Publication number||US7186814 B2|
|Application number||US 10/291,291|
|Publication date||6 Mar 2007|
|Filing date||8 Nov 2002|
|Priority date||9 Nov 2001|
|Also published as||CA2466656A1, CA2466656C, DE60228128D1, EP1466015A2, EP1466015A4, EP1466015B1, US20030143598, WO2003081202A2, WO2003081202A3|
|Publication number||10291291, 291291, US 7186814 B2, US 7186814B2, US-B2-7186814, US7186814 B2, US7186814B2|
|Inventors||Viswanadham Garimella, James J. Storhoff|
|Original Assignee||Nanosphere, Inc.|
|Export Citation||BiBTeX, EndNote, RefMan|
|Patent Citations (77), Non-Patent Citations (87), Referenced by (24), Classifications (20), Legal Events (13)|
|External Links: USPTO, USPTO Assignment, Espacenet|
This application claims the benefit of priority from U.S. Provisional application No. 60/348,239, filed Nov. 9, 2001, which is herein incorporated by reference in its entirety.
The invention relates to stable bioconjugate-nanoparticle probes which are useful for detecting nucleic acids and other target analytes. The invention also relates to methods for preparing bioconjugate-nanoparticle probes, to methods of detecting target analytes using the probes, and to kits comprising the probes.
The development of methods for detecting and sequencing nucleic acids is critical to the diagnosis of genetic, bacterial, and viral diseases. See Mansfield, E. S. et al. Molecular and Cellular Probes, 9, 145–156 (1995). DNA detection methods that employ gold nanoparticle probes, modified with oligonucleotides, to indicate the presence of a particular DNA are described in application number PCT/US00/17507, which is incorporated by reference herein in its entirety. Typically, oligonucleotides having sequences complementary to the nucleic acid to be detected are attached to a nanoparticle. The nanoparticle conjugate hybridized to the nucleic acid results in a detectable change resulting from the hybridization of the oligonucleotide on the nanoparticle to the nucleic acid target in solution.
In order to attach the oligonucleotide to the nanoparticle, the oligonucleotide, the nanoparticle or both, are functionalized. These methods are known in the art and include, for instance, the functionalization of oligonucleotides with alkanethiols at their 3′-termini or 5′-termini. Such functionalized nucleotides readily attach to gold nanoparticles.
A problem associated with nanoparticles derivatized with alkanethiol-oligonucleotides is that the oligonucleotides are easily detached from the nanoparticle surface when the system is heated above a certain temperature. Heating destabilizes and inactivates the nanoparticle-oligonucleotide probes. The oligonucleotides can also be displaced from the nanoparticle surface in the presence of other thiol containing compounds such as DTT.
There exists a need for oligonucleotide-nanoparticle probes, and bioconjugate-nanoparticle probes in general, that exhibit better anchoring of the oligonucleotide to the nanoparticle and are thus more stable and robust. Also needed are methods for preparing such complexes.
The invention provides a nanoparticle probe comprising a bioconjugate of formula (A) coupled to a nanoparticle:
n is 2–100;
m is 0–100;
X is a nucleotide, modified oligonucleotide, or a nucleic acid derivative;
Z is a nucleotide, modified oligonucleotide, or polyanion
Q is a recognition group. The bioconjugate is coupled to the nanoparticle through the sulfur groups (—SH).
The invention also provides a nanoparticle probe comprising a bioconjugate of formula (B) coupled to a nanoparticle:
wherein n, m, X, Z and Q are as defined above for bioconjugate (A), and each L is a linker formed by the coupling of two moieties selected from the group consisting of COOH, NH2, CHO, Cl, Br, I, NCO, NCS, allyl, and CH3CO2 −, or L is —C(═NH2Cl)(CH2)3 −. The bioconjugate is coupled to the nanoparticle through the sulfur groups (—SH).
The invention further provides a nanoparticle probe comprising a bioconjugate of formula (C) coupled to a nanoparticle:
wherein n, m, X, Z and Q are as defined above for bioconjugate (A), and R is an organic moiety such as an alkyl group such linear or branched C1–C8 alkyl, and wherein the bioconjugate is coupled to the nanoparticle through the disulfide groups (—S—S—).
The invention also provides a nanoparticle probe comprising a bioconjugate of formula (D) coupled to a nanoparticle:
wherein n, m, X, Z, L and Q are as defined above for bioconjugate (B), and wherein W is an aliphatic or aromatic group. The bioconjugate is coupled to the nanoparticle through the sulfur groups (—SH and S—S).
The invention also provides a nanoparticle probe comprising a bioconjugate of formula (E) coupled to a nanoparticle:
wherein n, m, X, Z and Q are as defined above for bioconjugate (A), and wherein W is an aliphatic or aromatic group. The bioconjugate is coupled to the nanoparticle through the sulfur groups (—SH and S—S).
The invention also provides a nanoparticle probe comprising a bioconjugate of formula (F) coupled to a nanoparticle:
wherein n, m, X, Z, L and Q are as defined above for bioconjugate (B), and wherein the bioconjugate is coupled to the nanoparticle through the sulfur groups.
The invention also provides a nanoparticle probe comprising a bioconjugate of formula (G) coupled to a nanoparticle:
wherein n, m, X, Z, L, W, R and Q are as defined above. The bioconjugate is coupled to the nanoparticle through the sulfur groups.
The invention also provides methods of preparing bioconjugate-nanoparticle probes, methods of detecting target analytes using the probes and kits comprising the probes of the invention.
As used herein, a “type of oligonucleotides” refers to a plurality of oligonucleotide molecules having the same sequence. A “type of” nanoparticles, particles, latex microspheres, etc. having oligonucleotides attached thereto refers to a plurality of nanoparticles having the same type(s) of oligonucleotides attached to them. “Nanoparticles having bioconjugates attached thereto” are also sometimes referred to as “nanoparticle-bioconjugate probes,” “nanoparticle probes,” “nano probes,” or just “probes.”
The bio conjugates of formula (A), (B), (C), (D), (E), (F), and (G) provide a solution to the problem of nanoparticle probe instability which results when the probe is heated or subjected to thiol containing compounds. Specifically, the invention permits two or more sulfur groups present on a bioconjugate to bind to the nanoparticle surface, which enhances the stability of the nanoparticle-bioconjugate binding. The resulting bioconjugate nanoparticle probes are stable towards heat and have increased resistance to displacement by thiol containing compounds such as DTT (dithiothreitol).
The bioconjugates that are linked to nanoparticles to form the nanop article probes of the invention are of the formulae:
wherein n, m, X, Z, L, R, W and Q are as defined above.
As indicated above, Q represents a recognition group. By “recognition group” is meant at least one binding moiety with a binding affinity for a target analyte, such as a nucleic acid. Thus, the binding moiety may be, for example, one member of a recognition couple which consists of two or more substances having a binding affinity of one to the other. When a bioconjugate is bound to a nanoparticle, therefore, it provides useful biorecognition properties to the nanoparticle for the analyte. If the target is a nucleic acid, for example, the recognition group can bind to the nucleic acid by hybridization with the nucleic acid. The nucleic acid bound nanoparticle can then be detected.
Examples of recognition groups include, without limitation, a receptor, a nucleotide, a nucleoside, a polynucleotide, an oligonucleotide, double stranded DNA, a protein, an antibody, a peptide, a carbohydrate, a sugar, a hapten, a nucleic acid, an amino acid, a peptide nucleic acid, a linked nucleic acid, a nucleoside triphosphate, a lipid, a lipid bound protein, an aptamer, a virus, a cell fragment, or a whole cell. Examples of recognition group-target analyte couples include: an antigen and an antibody; an antigen and an antibody derivative with a complementary antigen-binding domain; sugar and a lectin; a receptor and a ligand; a nucleotide sequence and a complementary nucleotide sequence; a nucleotide sequence and its binding protein or synthetic binding agent; a biotin and avidin or streptavidin; cellulose or chitin and cellulose binding domain. A preferred recognition group is an oligonucleotide. Also preferred is an antibody.
The recognition group can also be an oligonucleotide having a sequence that is complementary to at least a portion of a second oligonucleotide having a second recognition group, e.g., an oligonucleotide sequence or protein, bound thereto. The second recognition group can then be used for specific binding to a target analyte, e.g., an antigen.
The recognition group can also be a first recognition group, e.g., biotin, that can bind to a second recognition group, e.g., streptavidin, that is a member of the recognition couple. The second recognition group can then be bound directly or indirectly (e.g., via a linker) to a third recognition group, e.g., a receptor, which can bind to a target analyte.
Z, when present, is a nucleotide spacer, a modified oligonucleotide, a polyanion, or other type of spacer which may be utilized in oligonucleotide synthesis such as a polyethylene glycol. It has been found that hybridization efficiency of nanoparticle-bioconjugate probes with nucleic acids can be increased by the use of a spacer portion between the recognition group on the bioconjugate and the nanoparticle. By using a spacer portion, the recognition group is spaced away from the surface of the nanoparticles and is more accessible for hybridization with its target. The length and sequence of the spacer portion providing good spacing of the recognition portion away from the nanoparticles can be determined empirically. It has been found that a spacer portion comprising at least about 10 nucleotides, preferably 10–50 nucleotides, gives good results. The spacer portion may have any sequence which does not interfere with the ability of the recognition group to become bound to a target analyte or a capture moiety on a surface in sandwich hybridization assays. For instance, the spacer portions should not have sequence complementary to each other, to that of the recognition group, or to that of the target analyte. Preferably, the bases of the nucleotides of the spacer portion are all adenines, all thymines, all cytidines, or all guanines, unless this would cause one of the problems just mentioned. More preferably, the bases are all adenines or all thymines. Most preferably the bases are all thymines. Spacer Z and recognition group Q can be attached together by a variety of techniques. For instance, they can be attached directly by a covalent linkage or indirectly by non-covalent linkage.
As a linker, L can be any desired chemical group. For instance, L can be a polymer (e.g., polyethylene glycol, polymethylene, protein, peptide, oligonucleotide, or nucleic acid), —COO—, —CH2(CH2)vCOO—, —OCO—, R1N(CH2)v—NR1—, —OC(CH2)v—, —(CH2)v—, —O—(CH2)v—O—, —R1N—(CH2)v—,
v is 0–30 and R1 is H or is G(CH2)v, wherein G is —CH3, —CHCH3, —COOH, —CO2(CH2)vCH3, —OH, or —CH2OH.
L is also a linker formed by the coupling of two moieties attached to molecules, the moieties selected from the group consisting of COOH, NH2, CHO, Cl, Br, I, NCO, NCS, allyl, and CH3CO2 −, or L is —C(═NH2Cl)(CH2)3 −.
W is an aliphatic or aromatic group on which sulfur moieties can be readily bound. For instance, W can be steroid. Preferably W is an epiandrosterone derivative, as described in example 9.
X represents a nucleotide that has been functionalized with a thiol group (as shown). Preferably, the X groups are all adenines, all thymines, all cytidines, or all guanines, more preferably, all adenines or all thymines, most preferably all thymines. In (X)n, n is 2–100. Preferably, n is 2–50, more preferable 2–20, more preferably 2–10. Functionalization of the X linkage with a thiol group can be carried out by a variety of techniques.
In one embodiment of the invention, either a complex (I) or complex (II) containing at least two reactive groups R2 is synthesized by incorporating nucleotide building blocks containing an R2 group during synthesis of the oligonucleotide. R2 can be COOH, NH2, CHO, F, Cl, Br, I, NCO, NCS, allyl, or CH3CO2 −. If R2 in complex (I) or (II) is an NH2, then a nucleotide derivative containing an NH2 group is prepared for incorporation into the oligonucleotide. Suitable amine modified nucleotide reagents for use in this aspect of the invention include, but are not limited to, C6-dT phosphoramidite (5′-Dimethoxytrityl-5-[N-(trifluoroacetylaminohexyl)-3-acrylimido]-2′-deoxyUridine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite), amino modifier C6-dC (5′-Dimethoxytrityl-N-dimethylformamidine-5-[N-(trifluoroacetylaminohexyl)-3-acrylimido]-2′-deoxy-Cytidine,3′-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite), and amino modifier C2-dT (5′-dimethoxytrityl-5-[N-(trifluoroacetylaminoethyl)-3-acrylimido]-2′-deoxy-Uridine,3′-[(2-cyanoethyl)-(N,N-di-isopropyl)]-phosphoramidite). These and other amino modifiers are commercially available, for example from Glen Research, Sterling, Va. A preferred amino modifier reagent is C6-dT.
Complex (I) or (II) is reacted with a thiolating reagent that is functionalized with a group capable of reacting with the R2 group on the complex and resulting in formation of a sulfur functionalized bioconjugate. Suitable thiolating reagents generally include thiol compounds possessing one or more functional groups capable of reacting with the R2 group of the complex. Such reagents include, but are not limited to, cystamine, and compounds of the formula SH(CH2)nY, wherein n is 1–20 and Y is COOH, NH2, CHO, F, Cl, Br, I, NCO, NCS, allyl, or CH3CO2 −. Another suitable thiolating reagent is 2-iminothiolane hydrochloride (Traut's Reagent), which is preferred when R2 in complex (I) or (II) is an amine. In a preferred aspect of this embodiment, fluorinated nucleotides are incorporated into an oligonucleotide sequence and treated with cystamine to provide disulfide units on the sequence (References (1) L. V. Nechev, I. Kozekov, C. M. Harris, and T. M. Harris, Chem Res Toxicol, 2001, 14, 1506–1512. (2) A. R. Diaz, R. Eritja, and R. G. Garcia, Nucleos Nucleot, 1997, 16, 2035–2051. (3) D. A. Erlanson, J. N. M. Glover, and G. L. Verdine, J. Amer. Chem. Soc., 1997, 119, 6927–6928). This preferred aspect is described in detail in Examples 7–9, below.
An alternative method of thiolating complex (I) or (II) is to use a thiolating reagent that is a combination of reagents. For instance, if R2 in complex (I) or (II) is NH2, then the complex can be treated with an amine reactive bifunctional crosslinker, such as CHO(CH2)nCHO, and an alkyl or aryl thiol amine, such as SH(CH2)nNH2 or SH(C6H4)NH2. In both the amine reactive bifunctional crosslinker and the alkyl thiol amine, n is independently 1–30. Preferably, the amine reactive bifunctional crosslinker is glutaraldehyde (i.e., n is 3). Also preferably, the alkyl thiol amine is mercaptoethylamine (i.e., n is 2). Other preferred crosslinkers include 1,4 phenylene diisothiocyanate, 1,6 dihexanoic acid, or 1,6 hexane diisocyanate.
In an alternative and more direct approach for preparing a thiol functionalized bioconjugate, a phosphoramidite containing an alkylthiol or other thiol based group is synthesized and used to prepare a bioconjugate of formula (A). An example of a phosphoramidite containing an alkylthiol group is described in Example 4, below, and is prepared according to the method of Glick et al., Tetrahedron Letters, 1993, 34, 5549–5552 which is incorporated herein by reference.
As indicated above, the invention provides bioconjugate nanoparticle probes that are useful for detecting target analytes. To form the probe, bioconjugates (A), (B), (C), (D), (E), (F), or (G) are connected to the surface of a nanoparticle through the sulfur linkages on the bioconjugate. Preferably, the connection is through at least two thiol groups per bioconjugate molecule. Various methods can be used to connect the bioconjugate to the nanoparticle. In fact, any suitable method for attaching a bioconjugate to a nanoparticle may be used. A preferred method for attaching an bioconjugate to a nanoparticle is based on an aging process described in U.S. application Ser. No. 09/344,667, filed Jun. 25, 1999; Ser. No. 09/603,830, filed Jun. 26, 2000; Ser. No. 09/760,500, filed Jan. 12, 2001; Ser. No. 09/820,279, filed Mar. 28, 2001; Ser. No. 09/927,777, filed Aug. 10, 2001; and in International application Nos. PCT/US97/12783, filed Jul. 21, 1997; PCT/US00/17507, filed Jun. 26, 2000; PCT/US01/01190, filed Jan. 12, 2001; PCT/US01/10071, filed Mar. 28, 2001, the disclosures of which are incorporated by reference in their entirety.
The aging process provides nanoparticle-bioconjugate probes with enhanced stability and selectivity. The method comprises providing bioconjugates having covalently bound thereto thiol functional groups, prepared as described above. The functionalized bioconjugates are contacted with the nanoparticles in water for a time sufficient to allow at least some of the bioconjugates to bind to the nanoparticles by means of the functional groups. Such times can be determined empirically. For instance, it has been found that a time of about 12–24 hours gives good results. Other suitable conditions for binding of the bioconjugates can also be determined empirically. For instance, a concentration of about 10–20 nM nanoparticles and incubation at room temperature gives good results.
Next, at least one salt is added to the water to form a salt solution. The salt can be any suitable water-soluble salt. For instance, the salt may be sodium chloride, lithium chloride, potassium chloride, cesium chloride, ammonium chloride, sodium nitrate, lithium nitrate, cesium nitrate, sodium acetate, lithium acetate, cesium acetate, ammonium acetate, a combination of two or more of these salts, or one of these salts in phosphate buffer. Preferably, the salt is added as a concentrated solution, but it could be added as a solid. The salt can be added to the water all at one time or the salt is added gradually over time. By “gradually over time” is meant that the salt is added in at least two portions at intervals spaced apart by a period of time. Suitable time intervals can be determined empirically.
The ionic strength of the salt solution must be sufficient to overcome at least partially the electrostatic repulsion of the bioconjugates from each other and, either the electrostatic attraction of the negatively-charged bioconjugates for positively-charged nanoparticles, or the electrostatic repulsion of the negatively-charged bioconjugates from negatively-charged nanoparticles. Gradually reducing the electrostatic attraction and repulsion by adding the salt gradually over time has been found to give the highest surface density of bioconjugates on the nanoparticles. Suitable ionic strengths can be determined empirically for each salt or combination of salts. A final concentration of sodium chloride of from about 0.1 M to about 3.0 M in phosphate buffer, preferably with the concentration of sodium chloride being increased gradually over time, has been found to give good results.
After adding the salt, the bioconjugates and nanoparticles are incubated in the salt solution for an additional period of time sufficient to allow sufficient additional bioconjugates to bind to the nanoparticles to produce the stable nanoparticle-bioconjugates probes. An increased surface density of the bioconjugates on the nanoparticles has been found to stabilize the probes. The time of this incubation can be determined empirically. A total incubation time of about 24–48, preferably 40 hours, has been found to give good results (this is the total time of incubation; as noted above; the salt concentration can be increased gradually over this total time). This second period of incubation in the salt solution is referred to herein as the “aging” step. Other suitable conditions for this “aging” step can also be determined empirically. For instance, incubation at room temperature and pH 7.0 gives good results. The solution is then centrifuged and the nanoparticle probes processed as desired. For instance, the solution can be centrifuged at 14,000 rpm in an Eppendorf Centrifuge 5414 for about 15 minutes to give a very pale pink supernatant containing most of the oligonucleotide (as indicated by the absorbance at 260 nm) along with 7–10% of the colloidal gold (as indicated by the absorbance at 520 nm), and a compact, dark, gelatinous residue at the bottom of the tube. The supernatant is removed, and the residue is resuspended in the desired buffer.
The probes produced by use of the “aging” step have been found to be considerably more stable than those produced without the “aging” step. As noted above, this increased stability is due to the increased density of the bioconjugates on the surfaces of the nanoparticles which is achieved by the “aging” step. The surface density achieved by the “aging” step will depend on the size and type of nanoparticles and on the length, sequence and concentration of the oligonucleotides. A surface density adequate to make the nanoparticles stable and the conditions necessary to obtain it for a desired combination of nanoparticles and oligonucleotides can be determined empirically.
Oligonucleotides or other recognition elements containing multiple thiol moieties as described above may bind to a variety of nanoparticles that have an affinity for thiol groups. Nanoparticles useful in the practice of the invention include metal (e.g., gold, silver, platinum, cobalt), semiconductor (e.g., Si, CdSe, CdS, and CdS or CdSe coated with ZnS), core shell particles (e.g., gold coated silver particles), alloy particles (e.g. silver and gold alloy), magnetic (e.g., cobalt), and non metallic (e.g. silicon) colloidal materials. Core shell particles are described in PCT applications PCT/US01/50825, and PCT/US02/16382, as well as copending U.S. application Ser. Nos. 10/153,483 and 10/034,451, each of which is incorporated herein by reference. Other nanoparticles composed of materials that have an affinity for thiol groups may also be used. In addition, nanowires or nanorods having a composition with an affinity for thiol groups also may be used. The size of the nanoparticles is preferably from about 5 nm to about 150 nm (mean diameter), more preferably from about 5 to about 50 nm, most preferably from about 10 to about 30 nm.
Methods of making metal, semiconductor and magnetic nanoparticles are well-known in the art. See, e.g., Schmid, G. (ed.) Clusters and Colloids (V C H, Weinheim, 1994); Hayat, M. A. (ed.) Colloidal Gold: Principles, Methods, and Applications (Academic Press, San Diego, 1991); Massart, R., IEEE Transactions On Magnetics, 17, 1247 (1981); Ahmadi, T. S. et al., Science, 272, 1924 (1996); Henglein, A. et al., J. Phys. Chem., 99, 14129 (1995); Curtis, A. C., et al., Angew. Chem. Int. Ed. Engl., 27, 1530 (1988). Methods of making ZnS, ZnO, TiO2, AgI, AgBr, HgI2, PbS, PbSe, ZnTe, CdTe, In2S3, In2Se3, Cd3P2, Cd3As2, InAs, and GaAs nanoparticles are also known in the art. See, e.g., Weller, Angew. Chem. Int. Ed. Engl., 32, 41 (1993); Henglein, Top. Curr. Chem., 143, 113 (1988); Henglein, Chem. Rev., 89, 1861 (1989); Brus, Appl. Phys. A., 53, 465 (1991); Bahncmann, in Photochemical Conversion and Storage of Solar Energy (eds. Pelizetti and Schiavello 1991), page 251; Wang and Herron, J. Phys. Chem., 95, 525 (1991); Olshavsky et al., J. Am. Chem. Soc., 112, 9438 (1990); Ushida et al., J. Phys. Chem., 95, 5382 (1992).
Suitable nanoparticles are also commercially available from, e.g., Ted Pella, Inc. (gold), Amersham Corporation (gold) and Nanoprobes, Inc. (gold). Presently preferred nanoparticles are gold nanoparticles.
The bioconjugate-nanoparticle probes of the invention can be used to detect target analytes, such as nucleic acids. Examples of nucleic acids that can be detected with nanoparticle probes of the invention include genes (e.g., a gene associated with a particular disease), viral RNA and DNA, bacterial DNA, fungal DNA, cDNA, mRNA, RNA and DNA fragments, oligonucleotides, synthetic oligonucleotides, modified oligonucleotides, single-stranded and double-stranded nucleic acids, natural and synthetic nucleic acids, etc. Thus nanoparticle probes prepared according to the invention can be used, for example, for the diagnosis and/or monitoring of viral diseases (e.g., human immunodeficiency virus, hepatitis viruses, herpes viruses, cytomegalovirus, and Epstein-Barr virus), bacterial diseases (e.g., tuberculosis, Lyme disease, H. pylori, Escherichia coli infections, Legionella infections, Mycoplasma infections, Salmonella infections), sexually transmitted diseases (e.g., gonorrhea), inherited disorders (e.g., cystic fibrosis, Duchene muscular dystrophy, phenylketonuria, sickle cell anemia), and cancers (e.g., genes associated with the development of cancer); in forensics; in DNA sequencing; for paternity testing; for cell line authentication; for monitoring gene therapy; and for many other purposes.
To perform an assay according to the invention, a sample suspected of containing a target analyte is contacted with bioconjugate nanoparticle probes having attached thereto recognition groups capable of binding to at least a portion of the target analyte. The target to be detected may be isolated by known methods, or may be detected directly in cells, tissue samples, biological fluids (e.g., saliva, urine, blood, serum), solutions containing PCR components, solutions containing large excesses of oligonucleotides or high molecular weight DNA, and other samples, as also known in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd ed. 1989) and B. D. Hames and S. J. Higgins, Eds., Gene Probes 1 (IRL Press, New York, 1995). Methods of preparing nucleic acids for detection with hybridizing probes are well known in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd ed. 1989) and B. D. Hames and S. J. Higgins, Eds., Gene Probes 1 (IRL Press, New York, 1995).
If a nucleic acid is present in small amounts, it may be amplified by methods known in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd ed. 1989) and B. D. Hames and S. J. Higgins, Eds., Gene Probes 1 (IRL Press, New York, 1995). Preferred is polymerase chain reaction (PCR) amplification.
One method according to the invention for detecting nucleic acid comprises contacting a nucleic acid with one or more types of nanoparticle probes of the invention. The nucleic acid to be detected has at least two portions. The lengths of these portions and the distance(s), if any, between them are chosen so that when the bioconjugates on the nanoparticles hybridize to the nucleic acid, a detectable change occurs. These lengths and distances can be determined empirically and will depend on the type of particle used and its size and the type of electrolyte which will be present in solutions used in the assay (as is known in the art, certain electrolytes affect the conformation of nucleic acids).
Also, when a nucleic acid is to be detected in the presence of other nucleic acids, the portions of the nucleic acid to which the bioconjugates on the nanoparticles are to bind must be chosen so that they contain sufficient unique sequence so that detection of the nucleic acid will be specific. Guidelines for doing so are well known in the art.
Although nucleic acids may contain repeating sequences close enough to each other so that only one type of bioconjugate-nanoparticle conjugate need be used, this will be a rare occurrence. In general, the chosen portions of the nucleic acid will have different sequences and will be contacted with nanoparticles carrying two or more different bioconjugates, preferably attached to different nanoparticles. Additional portions of the DNA could be targeted with corresponding nanoparticles. Targeting several portions of a nucleic acid increases the magnitude of the detectable change.
The contacting of the nanoparticle-bioconjugate probes with the nucleic acid takes place under conditions effective for hybridization of the bioconjugates on the nanoparticles with the target sequence(s) of the nucleic acid. These hybridization conditions are well known in the art and can readily be optimized for the particular system employed. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd ed. 1989). Preferably stringent hybridization conditions are employed.
Faster hybridization can be obtained by freezing and thawing a solution containing the nucleic acid to be detected and the nanoparticle-bioconjugate probes. The solution may be frozen in any convenient manner, such as placing it in a dry ice-alcohol bath for a sufficient time for the solution to freeze (generally about 1 minute for 100 microliters of solution). The solution must be thawed at a temperature below the thermal denaturation temperature, which can conveniently be room temperature for most combinations of nanoparticle-bioconjugate probes and nucleic acids. The hybridization is complete, and the detectable change may be observed, after thawing the solution.
The rate of hybridization can also be increased by warming the solution containing the nucleic acid to be detected and the nanoparticle-bioconjugate probes to a temperature below the dissociation temperature (Tm) for the complex formed between the bioconjugates on the nanoparticles and the target nucleic acid. Alternatively, rapid hybridization can be achieved by heating above the dissociation temperature (Tm) and allowing the solution to cool.
The rate of hybridization can also be increased by increasing the salt concentration (e.g., from 0.1 M to 1 M NaCl).
The detectable change that occurs upon hybridization of the bioconjugates on the nanoparticles to the nucleic acid may be an optical change (e.g. color change), the formation of aggregates of the nanoparticles, or the precipitation of the aggregated nanoparticles. The optical changes can be observed with the naked eye or spectroscopically. The formation of aggregates of the nanoparticles can be observed by electron microscopy or by nephelometry. The precipitation of the aggregated nanoparticles can be observed with the naked eye or microscopically. Preferred are color changes observable with the naked eye.
The observation of a color change with the naked eye can be made more readily against a background of a contrasting color. For instance, when gold nanoparticles are used, the observation of a color change is facilitated by spotting a sample of the hybridization solution on a solid white surface (such as silica or alumina TLC plates, filter paper, cellulose nitrate membranes, and nylon membranes, preferably a nylon membrane) and allowing the spot to dry. Initially, the spot retains the color of the hybridization solution (which ranges from pink/red, in the absence of hybridization, to purplish-red/purple, if there has been hybridization). On drying at room temperature or 80° C. (temperature is not critical), a blue spot develops if the nanoparticle-bioconjugate probes had been linked by hybridization with the target nucleic acid prior to spotting. In the absence of hybridization (e.g., because no target nucleic acid is present), the spot is pink. The blue and the pink spots are stable and do not change on subsequent cooling or heating or over time. They provide a convenient permanent record of the test. No other steps (such as a separation of hybridized and unhybridized nanoparticle-bioconjugate probes) are necessary to observe the color change. The color change may be quantitated by recording the plate image with an optical scanning device such as a flatbed scanner or CCD camera, and analyzing the amount and type of color of each individual spot. Alternatively, a color filter (e.g. red filter) may be used to filter out specific colors so that the signal intensity of each spot may be recorded and analyzed.
An alternate method for easily visualizing the assay results is to spot a sample of nanoparticle probes hybridized to a target nucleic acid on a glass fiber filter (e.g., Borosilicate Microfiber Filter, 0.7 micron pore size, grade FG75, for use with gold nanoparticles 13 nm in size), while drawing the liquid through the filter. Subsequent rinsing with water washes the excess, non-hybridized probes through the filter, leaving behind an observable spot comprising the aggregates generated by hybridization of the nanoparticle probes with the target nucleic acid (retained because these aggregates are larger than the pores of the filter). This technique may provide for greater sensitivity, since an excess of nanoparticle probes can be used.
Some embodiments of the method of detecting nucleic acid utilize a substrate. By employing a substrate, the detectable change (the signal) can be amplified and the sensitivity of the assay increased.
Any substrate can be used which allows observation of the detectable change. Suitable substrates include transparent solid surfaces (e.g., glass, quartz, plastics and other polymers), opaque solid surface (e.g., white solid surfaces, such as TLC silica plates, filter paper, glass fiber filters, cellulose nitrate membranes, nylon membranes), and conducting solid surfaces (e.g., indium-tin-oxide (ITO)). The substrate can be any shape or thickness, but generally will be flat and thin. Preferred are transparent substrates such as glass (e.g., glass slides) or plastics (e.g., wells of microtiter plates).
In one embodiment oligonucleotides are attached to the substrate. The oligonucleotides can be attached to the substrates as described in, e.g., Chrisey et al., Nucleic Acids Res., 24, 3031–3039 (1996); Chrisey et al., Nucleic Acids Res., 24, 3040–3047 (1996); Mucic et al., Chem. Commun., 555 (1996); Zimmermann and Cox, Nucleic Acids Res., 22, 492 (1994); Bottomley et al., J. Vac. Sci. Technol. A, 10, 591 (1992); and Hegner et al., FEBS Lett., 336, 452 (1993).
The oligonucleotides attached to the substrate have a sequence complementary to a first portion of the sequence of a nucleic acid to be detected. The nucleic acid is contacted with the substrate under conditions effective to allow hybridization of the oligonucleotides on the substrate with the nucleic acid. In this manner the nucleic acid becomes bound to the substrate. Any unbound nucleic acid is preferably washed from the substrate before adding nanoparticle-bioconjugate probes.
Next, the nucleic acid bound to the substrate is contacted with a first type of nanoparticles having bioconjugates, such as oligonucleotides, attached thereto. The oligonucleotides have a sequence complementary to a second portion of the sequence of the nucleic acid, and the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid. In this manner the first type of nanoparticles become bound to the substrate. After the nanoparticle-oligonucleotide conjugates are bound to the substrate, the substrate is washed to remove any unbound nanoparticle-oligonucleotide conjugates and nucleic acid.
The oligonucleotides on the first type of nanoparticles may all have the same sequence or may have different sequences that hybridize with different portions of the nucleic acid to be detected. When oligonucleotides having different sequences are used, each nanoparticle may have all of the different oligonucleotides attached to it or, preferably, the different oligonucleotides are attached to different nanoparticles. Alternatively, the oligonucleotides on each of the first type of nanoparticles may have a plurality of different sequences, at least one of which must hybridize with a portion of the nucleic acid to be detected.
The first type of nanoparticle-oligonucleotide conjugates bound to the substrate is optionally contacted with a second type of nanoparticles having oligonucleotides attached thereto. These oligonucleotides have a sequence complementary to at least a portion of the sequence(s) of the oligonucleotides attached to the first type of nanoparticles, and the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the first type of nanoparticles with those on the second type of nanoparticles. After the nanoparticles are bound, the substrate is preferably washed to remove any unbound nanoparticle-oligonucleotide conjugates.
The combination of hybridizations produces a detectable change. The detectable changes are the same as those described above, except that the when second type of conjugates, multiple hybridizations result in an amplification of the detectable change. In particular, since each of the first type of nanoparticles has multiple oligonucleotides (having the same or different sequences) attached to it, each of the first type of nanoparticle-oligonucleotide conjugates can hybridize to a plurality of the second type of nanoparticle-oligonucleotide conjugates. Also, the first type of nanoparticle-oligonucleotide conjugates may be hybridized to more than one portion of the nucleic acid to be detected. The amplification provided by the multiple hybridizations may make the change detectable for the first time or may increase the magnitude of the detectable change. This amplification increases the sensitivity of the assay, allowing for detection of small amounts of nucleic acid.
If desired, additional layers of nanoparticles can be built up by successive additions of the first and second types of nanoparticle-oligonucleotide conjugates. In this way, the number of nanoparticles immobilized per molecule of target nucleic acid can be further increased with a corresponding increase in intensity of the signal.
In one embodiment for detection of non-nucleic acid analytes (see for example U.S. patent application Ser. No. 09/820,279, filed Mar. 28, 2001, and International application PCT/01/10071, filed Mar. 28, 2001, each of which is incorporated herein by reference) the analyte may be bound directly or indirectly, via covalent or non-covalent interactions, to a substrate. The substrates are rthe same type as described above. For indirect binding, the analyte can be bound to the substrate via a linker, e.g., an oligonucleotide or other spacer molecule. Alternatively, the analyte may be modified by binding it to an oligonucleotide having a sequence that is complementary to at least a portion of the sequence of a capture oligonucleotide bound to a substrate. The nanoparticle-probe having a recognition group for the analyte is then contacted with the substrate under conditions effective to allow the specific binding of the nanoparticle-probe to the analyte bound to the substrate and the presence of the analyte can be visually detected either by formation of a spot on the substrate or through the use of staining material such as silver on gold stain. See
In another method for detecting analytes, the target analyte can be modified by attaching the analyte to the nanoparticle-probe as the recognition portion of the probe. Thereafter, the modified nanoparticle-probe is contacted with a substrate having a second member of the recognition couple bound thereto. The presence of the analyte can be visually detected either by formation of a spot on the substrate or through the use of staining material such as silver on gold stain.
In yet another method for detecting analytes, the target analyte is modified by binding it to an oligonucleotide having a sequence that is complementary to at least a portion of a sequence of an oligonucleotide (recognition group) bound to the nanoparticle-probe. The modified target is then coupled to the nanoparticle-probe by contacting the modified target and the nanoparticle-probe under conditions effective for hybridization between the oligonucleotide bound to the target and the oligonucleotide bound to the nanoparticle-probe. The hybridized complex is then contacted with a substrate having a recognition group for the analyte bound thereto. The presence of the analyte can be visually detected either by formation of a spot on the substrate or through the use of staining material such as silver on gold stain. See
When a substrate is employed, a dectectable change can be produced or enhanced by staining. Staining material, e.g., gold, silver, etc., can be used to produce or enhance a detectable change in any assay performed on a substrate, including those described above. For instance, silver staining can be employed with any type of nanoparticles that catalyze the reduction of silver. Preferred are nanoparticles made of noble metals (e.g., gold and silver). See Bassell, et al., J. Cell Biol., 126, 863–876 (1994); Braun-Howland et al., Biotechniques, 13, 928–931 (1992). If the nanoparticles being employed for the detection of analyte do not catalyze the reduction of silver, then silver ions can be complexed to the target analyte to catalyze the reduction. See Braun et al., Nature, 391, 775 (1998). Also, silver stains are known which can react with the phosphate groups on nucleic acids.
An alternate method for utilizing the polythiol nanoparticle probes is in the application to micro arrays for detecting a variety of biomolecules such as nucleic acids, proteins or carbohydrates. One specific example is the application of polythiol modified oligonucleotide labeled gold nanoparticle probes to the detection of nucleic acids in a sandwich assay format as described in U.S. Pat. No. 6,361,944. In this method, the gold nanoparticle labels are detected via a silver deposition process. Alternatively, a gold nanoparticle development procedure may be used as described in U.S. Pat. No. 6,417,340 and detected optically. It should be noted that the polythiol nanoparticle probes described herein also can be applied as detection probes for use as in situ hybridization labels or expanded to other DNA/RNA detection technologies.
The invention further provides a kit for performing the assays for detecting or quantitating analytes. The kit comprises a container holding nanoparticle probes having recognition groups attached to them. The kit may also contain other reagents and items useful for performing the assays. The reagents may include controls, standards, PCR reagents, hybridization reagents, buffers, etc. Other items which be provided as part of the kit include reaction devices (e.g., test tubes, microtiter plates, solid surfaces (possibly having a capture molecule attached thereto), syringes, pipettes, cuvettes, containers, etc.
The following examples are illustrative of the invention but do not serve to limit its scope.
In this example, amino modifier C6-DT groups are introduced into an oligonucleotide using an amino modifier phosphoramidite (available from Glen Research, Sterling, Va.) (
Protocol. The amino modifier C6-dT reacts in a manner identical to normal phosphoramidites, i.e., standard automated oligonucleotide synthesis. The trifluoroacetyl (TFA) protecting group on the primary amine is removed during standard ammonium hydroxide deprotection. However, a minor side reaction during ammonia deprotection can lead to irreversibly capping 2–5% of the amine. To prevent this reaction, the synthesis is carried out using acetyl-protected dC and deprotection is carried out in 30% ammonia/40% methylamine 1:1 (AMA) at 65° C. for 15 minutes.
In this example, the amine containing oligonucleotide prepared in Example 1 is reacted with 2-iminothiolane.HCl (Traut's Reagent, available from Pierce Chemical Company, Rockford, Ill.) to introduce thiol groups (
Protocol. The amine containing oligonucleotide prepared in Example 1 is first purified by reverse phase HPLC and is then dissolved in 50 mM triethanolamine-HCl buffer of pH 8 (or other pH 8 buffer such as 0.16 M Borate of 10 mM phosphate). A 2–10 fold molar excess of 2-iminothiolane-HCl is added. The solution is incubated for 20–60 minutes at 0–25° C. The thiolated amine oligonucleotide is then separated from the amine oligonucleotide using reverse-phase HPLC (0.03 M TEAA buffer (pH 7) with a 1%/min gradient of 95:5 acetonitrile/0.03 M TEAA (pH 7)).
Alternatively, the following protocol can be used. The amine containing oligonucleotide is first purified by reverse-phase HPLC. After purification, the oligonucleotide is re-dissolved in a phosphate or borate buffer (pH 7.2–8.5) containing a 10–100 fold excess of water soluble carbodiimide (WSC, e.g., ethyl dimethylaminopropyl-carbodiimide) and a 10–100 fold excess of 3-mercaptopropionic acid and allowed to stand for 2–4 hours at room temperature. Next, the oligonucleotide is purified through a NAP-10 column to remove excess reagents and eluted in water, followed by reverse-phase HPLC purification.
This example presents an alternative method for introducing thiol groups into an oligonucleotide. An amine reactive bifunctional crosslinker, e.g., glutaraldehyde, and a heterobifunctional group such as an alkyl thiol amine are reacted with the amine functionalized oligonucleotide prepared in Example 2, to create thiol groups (
Protocol. The amine containing oligonucleotide is first purified be reverse-phase HPLC. After purification, the oligonucleotide is redissolved in a phosphate or borate buffer (pH 6–9) containing 10% glutaraldehyde and allowed to stand for 1–2 hours. Next, the oligonucleotide is purified through a NAP-10 column to remove excess glutaraldehyde and eluted in pH 6–9 phosphate or borate buffer. A 10–100 fold excess of mercaptoethylamine is then reacted with the oligonucleotide for 2–4 hours at room temperature, followed by addition of sodium cyanoborohydride to create a 10% solution for 5 min to reduce the Schiff base. The oligonucleotide is subsequently purified by reverse-phase HPLC.
In this example, a phosphoramidite of formula III (
An alternative protocol for the introduction of thiol groups into an oligonucleotide is as follows. Carboxy-dT (available from Glen Research, Sterling, Va.) is introduced into an oligonucleotide in an analogous manner to Example 1. Deprotection is carried out using mild deprotection: 0.4 M methanolic sodium hydroxide (methanol:water 4:1) for 17 hours at room temperature. The support is pipetted off and the solution neutralized with 2 M TEAA. DNA is purified by reverse phase HPLC. The DNA is resuspended in 100 mM MES buffer (pH 6), water soluble coupling reagents are added (ethyl dimethylaminopropyl-carbodiimide (EDC) and -N-hydroxysulfosuccinimide (sulfo NHS)) at a final concentration of 2 mM EDC and 5 mM sulfo-NHS, and the mixture incubated at room temperature for 15 min. Next, a thiol coupling reagent (e.g., SH(CH2)xNH2) is added at a 10 fold excess and the mixture incubated at room temperature for 3 hours. The oligonucleotide is purified through a NAP-10 column to remove excess reagents, followed by HPLC purification.
In this example the thiol functionalized oligonucleotide prepared by any of the methods disclosed herein is attached to a gold nanoparticle through at least two of the thiol groups.
Protocol. A 4 μM solution of a polythiol modified oligonucleotide is incubated with an approximately 15 nM gold particle dispersion and then the particles isolated by centrifugation.
Epiandrosterone can be used as an additional linking element. Its advantages include that it is a readily available, easily derivatized to a ketoalcohol and, as a substituent with a large hydrophobic surface, may help screen the approach of water soluble molecules to the gold surface (Letsinger, et al., J. Am. Chem. Soc. 115, 7535–7536—Bioconjugate Chem. 9, 826–830). Incorporation of the epi disulfide into an oligonucleotide is conducted by phosphoramidite chemistry, as described below.
The epi disulfide derivative has the structure:
(a) Synthesis of epi disulfide (
Recrystallization from pentane/ether afforded a white powder, mp 110–112° C.; 1H NMR, δ 3.6 (1H, C3OH), 3.54–3.39 (2H, m 2OCH of the dithiane ring), 3.2–3.0 (4H, m 2CH2S), 2.1–0.7 (29H, m steroid H); mass spectrum (ES+) calcd for C23H36O3S2 (M+H) 425.2179, found 425.2151. Anal. (C23H37O3S2)S: calcd, 15.12; found, 15.26.
(b) Preparation of Steroid-Disulfide Ketal Phosphoramidite Derivative (
Epi disulfide 1a (100 mg) was dissolved in THF (3 mL) and cooled in a dry ice alcohol bath. N,N-diisopropylethylamine (80 μL) and β-cyanoethyl chlorodiisopropylphosphoramidite (80 μL) were added successively; then the mixture was warmed to room temperature, stirred for 2 h, mixed with ethyl acetate (100 mL), washed with 5% aq. NaHCO3 and with water, dried over sodium sulfate, and concentrated to dryness. The residue was taken up in the minimum amount of dichloromethane, precipitated at −70° C. by addition of hexane, and dried under vacuum; yield 100 mg; 31P NMR 146.02.
5′-Modified oligonucleotides are constructed on CPG supports using conventional phosphoramidite chemistry, except that compound 1b is employed in the final phosphitilation step. Products are cleaved from the support by treatment with concentrated NH4OH for 16 h at 55° C. The oligonucleotides 1c are purified by reversed phase HPLC on a Dionex DX500 system equipped with a Hewlett Packard ODS Hypersil column (4.6×200 nm, 5 μm particle size) using TEAA buffer (pH 7.0) and a 1%/min gradient of 95% CH3CN/5% 0.03 TEAA at a flow rate of 1 mL/min.
In this example, fluorine modified Inosine nucleotides (2-F-dI; available from Glen Research, Sterling, Va.) are introduced into oligonucleotide 1c and treated with cystamine after completing synthesis. See L. V. Nechev, I. Kozekov, C. M. Harris, and T. M. Harris, Chem Res Toxicol, 2001, 14, 1506–1512; A. R. Diaz, R. Eritja, and R. G. Garcia, Nucleos Nucleot, 1997, 16, 2035–2051; D. A. Erlanson, J. N. M. Glover, and G. L. Verdine, J. Amer. Chem. Soc., 1997, 119, 6927–6928.
Protocol. 1. Incorporate 2-F-dI at the desired position using standard synthesis conditions with 2-F-dl-CE phosphoramidite (commercially available form Glen Research). 2. Nucleoside Conversion: At the conclusion of oligonucleotide synthesis, rinse the synthesis column with acetonitrile and roughly dry the support with argon. Dissolve desired primary amine in 1–2 mL DMSO (other organic solvent can be substituted depending on solubility of amine) at a concentration of 0.5 M. Treat the support in the column with the amine solution using two 1 mL disposable syringes. Incubate for 18–24 hours at RT to effect conversion. An alternate approach is to transfer the support to a Sarstedt tube, add the amine solution and incubate as above. 3. Preliminary O6 Deprotection: Wash the support 2 times with DMSO then 3 times with acetonitrile and roughly dry the support with argon. Using two disposable syringes as above, treat the support two times with 1 ml each 1M DBU in acetonitrile one hour each time. Rinse the support with 1 ml each of methanol X 2, and acetonitrile X 3. Roughly dry the support with argon and deprotect the oligo 1d from the support using ammonium hydroxide as normal.
Stability of the nanoparticle probes of the invention was evaluated by spotting the subject mixtures on a solid white surface (such as a C-18 silica TLC plate or a reversed phase (RP) HPLC plate) and observing the color of the spot after drying. Red indicates starting nanoparticle with DNA strands on dispersed in solution, and violet indicates particle aggregation due to partial displacement of oligonucleotides on the gold nanoparticle, and blue indicates even greater particle aggregation due to more extensive displacement of oligonucleotides.
Oligonucleotides having the sequence 5′-Epi-SH-SH-al 8-gcg gaa gaa tgt gtc-3′ [SEQ ID NO:1] were prepared as described in Examples 7–9. These oligonucleotides have an analogous structure to oligonucleotides 1d in
EPI+2S probes are prepared (loaded) in two different salt solutions; the same oligonucleotide is loaded in either 0.85 M sodium chloride or in 2.2 M sodium chloride. The EPI-2S probes' length is 35 mer total and contains no fillers.
Attachment of Oligonucleotides to Gold Nanoparticles
A colloidal solution of citrate stabilized gold nanoparticles (about 10 nM), prepared by the citrate reduction method (Grabar et. al, Anal. Chem. 1995, 67, 735.), was mixed with sulfur modified-a20-probe oligonucleotide (4 μM), and allowed to stand for 24 hours at room temperature in 1 ml Eppendorf capped vials. Then, Step 1: 100 μL of a 0.1 M sodium hydrogen phosphate buffer, pH 7.0, and 100 μL of 1.0 M NaCl were premixed and added to the solution and allowed to stand for an additional 12 hours. Step2: Then the salt concentration was increased to 0.3M NaCl and kept further 12 h at room temperature. Step 3: At this point the salt concentration was increased to 0.85 and kept another 16 h at room temperature. Total salt aging process took 40 h. In the case of the 2.2 M salt concentration, work up at the stage of step 3 salt was increased gradually to 2.2 M NaCl and kept at room temperature.
The solution was next centrifuged at 14,000 rpm in an Eppendorf Centrifuge 5414 for about 15 minutes to give a very pale pink supernatant containing most of the oligonucleotide (as indicated by the absorbance at 260 nm) along with 7–10% of the colloidal gold (as indicated by the absorbance at 520 nm), and a compact, dark, gelatinous residue at the bottom of the tube. The supernatant was removed, and the residue was re suspended in the desired buffer.
Oligonucleotides having an analogous structure to oligonucleotide 1c, i.e., possessing an epi disulfide linkage but no other sulfur groups, were prepared as described in Examples 7–8. The probe length is 18mer+A20 linker and total 38mer. The probe sequence is 5′-Epi-a20-cct caa aga aaa g-3′ [SEQ ID NO:2] and A20-Epi filler. The probe is loaded in 0.85 M NaCl solution. These probes are representative of prior art probes in that they do not contain additional thiol functionalization of the oligonucleotide backbone. The probes are denoted “EPI probes.”
Attachment of Oligonucleotides to Gold Nanoparticles:
A colloidal solution of citrate stabilized gold nanoparticles (about 10 nM), prepared by the citrate reduction method (Grabar et. al, Anal. Chem. 1995, 67, 735.) was mixed with sulfur modified-a20-probe oligonucleotide and corresponding sulfur modified-da20 filler oligonucleotide (each to a concentration of 1.7 μM), prepared as described in part B, and allowed to stand for 24 hours at room temperature in 1 ml Eppendorf capped vials. Then, Step 1: 100 μL of a 0.1 M sodium hydrogen phosphate buffer, pH 7.0, and 100 μL of 1.0 M NaCl were premixed and added to the solution and allowed to stand for an additional 12 hours. Step2: Then salt concentration was increased to 0.3M NaCl and kept further 12 h at room temperature. Step 3: At this point salt concentration was increased to 0.85 and kept another 16 h at room temperature. Total salt aging process took 40 h.
The solution was next centrifuged at 14,000 rpm in an Eppendorf Centrifuge 5414 for about 15 minutes to give a very pale pink supernatant containing most of the oligonucleotide (as indicated by the absorbance at 260 nm) along with 7–10% of the colloidal gold (as indicated by the absorbance at 520 nm), and a compact, dark, gelatinous residue at the bottom of the tube. The supernatant was removed, and the residue was resuspended in the desired buffer.
This example verified that EPI+2S probes, like EPI probes, bind to a target.
To 100 μl of a colloid mixture (50 μl of EPI+2S probes and 50 μl of EPI probes), 1 μl of a 10 μM solution of the target (MTHFR 87 mer synthetic target) was added and the sample frozen at −70° C. for 1 minute and then thawed at room temperature. After the sample was brought to room temperature, 3 μl aliquots were spotted on a RP HPLC plate and solvents evaporated. Simultaneously, control solution prepared in a similar manner but without target was spotted on the HPLC plate. After evaporation of the solvents, the target containing spot turned completely blue, indicating hybridizing to the target. The control spot turned red, indicating absence of hybridization. See
This example shows the increased stability of EPI+2S probes in DTT solution, in comparison to EPI probes. The example also shows that EPI+2S probes prepared in 2.2 M NaCl solution (“2.2 M EPI+2S probes”) are more stable than EPI+2S probes prepared in 0.85 M NaCl solution (“0.85 M EPI+2S probes”).
To 50 μl of the probe colloid in 0.1 M NaCl and 10 mM Phosphate buffer at pH 7, 5 μl of 0.1M DTT solution was added and the mixture spotted on a C-18 RP silica plate. The EPI probe spot turned blue in 44 h. The 0.85 M loading EPI+2S probe spot turned blue within 72 h, indicating greater stability than the EPI probes. As expected, the 2.2 M loading EPI+2S probe spot did not turn blue even after 83 h in 0.1M NaCl conditions, indicating even greater stability. See
This example reveals the increased stability of EPI+2S probes in the presence of DTT at elevated temperature, compared with EPI probes.
To 50 μl of the colloid, 5 μl of 0.1M DTT solution was added and incubated at 60° C. and spotted on a C-18 RP silica plate. The EPI probe turned blue in 70 min, whereas the 0.85 M EPI-2S probe started turning blue at 120 min. See
This example shows the increased stability of EPI+2S probes in the presence of DTT and MgCl2 at elevated temperature, compared with EPI probes.
To 50 μl of the colloid, 5 μl of 0.1 M DTT solution and 10 mM MgCl2 [final concentration] were added and the samples incubated at 60° C. The samples were spotted on a C-18 RP silica plate. The EPI probe spot turned blue in 25 min while the 0.85 M EPI-2S probe spot started turning blue at 25 min. The 2.2 M EPI-2S probe spot also started turning blue at 25 min. See
|Cited Patent||Filing date||Publication date||Applicant||Title|
|US4193983||16 May 1978||18 Mar 1980||Syva Company||Labeled liposome particle compositions and immunoassays therewith|
|US4256834||9 Apr 1979||17 Mar 1981||Syva Company||Fluorescent scavenger particle immunoassay|
|US4261968||10 May 1979||14 Apr 1981||Syva Company||Fluorescence quenching with immunological pairs in immunoassays|
|US4313734||13 Jul 1979||2 Feb 1982||Akzona Incorporated||Metal sol particle immunoassay|
|US4318707||3 Jun 1980||9 Mar 1982||Syva Company||Macromolecular fluorescent quencher particle in specific receptor assays|
|US4650770||7 Dec 1983||17 Mar 1987||Syntex (U.S.A.) Inc.||Energy absorbing particle quenching in light emitting competitive protein binding assays|
|US4713348||22 Oct 1985||15 Dec 1987||Syntex (U.S.A.) Inc.||Fluorescent multiparameter particle analysis|
|US4853335||28 Sep 1987||1 Aug 1989||Olsen Duane A||Colloidal gold particle concentration immunoassay|
|US4868104||6 Sep 1985||19 Sep 1989||Syntex (U.S.A.) Inc.||Homogeneous assay for specific polynucleotides|
|US4996143||13 Apr 1990||26 Feb 1991||Syngene, Inc.||Fluorescent stokes shift probes for polynucleotide hybridization|
|US5225064||6 Mar 1992||6 Jul 1993||Enzyme Technology Research Group, Inc.||Peroxidase colloidal gold oxidase biosensors for mediatorless glucose determination|
|US5284748||10 Apr 1992||8 Feb 1994||Immunotronics, Inc.||Method for electrical detection of a binding reaction|
|US5288609||30 Oct 1992||22 Feb 1994||Enzo Diagnostics, Inc.||Capture sandwich hybridization method and composition|
|US5294369||5 Dec 1990||15 Mar 1994||Akzo N.V.||Ligand gold bonding|
|US5360895||9 Dec 1992||1 Nov 1994||Associated Universities, Inc.||Derivatized gold clusters and antibody-gold cluster conjugates|
|US5384073||21 Jan 1994||24 Jan 1995||Akzo N.V.||Ligand gold bonding|
|US5384265||26 Mar 1993||24 Jan 1995||Geo-Centers, Inc.||Biomolecules bound to catalytic inorganic particles, immunoassays using the same|
|US5460831||4 Nov 1993||24 Oct 1995||The Regents Of The University Of California||Targeted transfection nanoparticles|
|US5472881||21 Mar 1994||5 Dec 1995||University Of Utah Research Foundation||Thiol labeling of DNA for attachment to gold surfaces|
|US5514602||25 Feb 1993||7 May 1996||Ortho Diagnostic Systems, Inc.||Method of producing a metal sol reagent containing colloidal metal particles|
|US5521289 *||29 Jul 1994||28 May 1996||Nanoprobes, Inc.||Small organometallic probes|
|US5543158||23 Jul 1993||6 Aug 1996||Massachusetts Institute Of Technology||Biodegradable injectable nanoparticles|
|US5571726||19 May 1995||5 Nov 1996||Ortho Diagnostic Systems, Inc.||Kit containing glutaraldehyde coated colloidal metal particles of a preselected size|
|US5599668||22 Sep 1994||4 Feb 1997||Abbott Laboratories||Light scattering optical waveguide method for detecting specific binding events|
|US5609907||9 Feb 1995||11 Mar 1997||The Penn State Research Foundation||Self-assembled metal colloid monolayers|
|US5637508||23 Jan 1995||10 Jun 1997||Geo-Centers, Inc.||Biomolecules bound to polymer or copolymer coated catalytic inorganic particles, immunoassays using the same and kits containing the same|
|US5665582||18 Apr 1994||9 Sep 1997||Dekalb Genetics Corp.||Isolation of biological materials|
|US5681943||8 May 1995||28 Oct 1997||Northwestern University||Method for covalently linking adjacent oligonucleotides|
|US5751018||29 Apr 1994||12 May 1998||The Regents Of The University Of California||Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers|
|US5830986||28 Oct 1996||3 Nov 1998||Massachusetts Institute Of Technology||Methods for the synthesis of functionalizable poly(ethylene oxide) star macromolecules|
|US5900481||6 Nov 1996||4 May 1999||Sequenom, Inc.||Bead linkers for immobilizing nucleic acids to solid supports|
|US5939021||23 Jan 1997||17 Aug 1999||Hansen; W. Peter||Homogeneous binding assay|
|US5990479||25 Nov 1997||23 Nov 1999||Regents Of The University Of California||Organo Luminescent semiconductor nanocrystal probes for biological applications and process for making and using such probes|
|US6025202||16 Dec 1998||15 Feb 2000||The Penn State Research Foundation||Self-assembled metal colloid monolayers and detection methods therewith|
|US6149868||28 Oct 1998||21 Nov 2000||The Penn State Research Foundation||Surface enhanced raman scattering from metal nanoparticle-analyte-noble metal substrate sandwiches|
|US6203989||25 Mar 1999||20 Mar 2001||Affymetrix, Inc.||Methods and compositions for amplifying detectable signals in specific binding assays|
|US6214560||18 Apr 1997||10 Apr 2001||Genicon Sciences Corporation||Analyte assay using particulate labels|
|US6251303||18 Sep 1998||26 Jun 2001||Massachusetts Institute Of Technology||Water-soluble fluorescent nanocrystals|
|US6277489||4 Dec 1998||21 Aug 2001||The Regents Of The University Of California||Support for high performance affinity chromatography and other uses|
|US6306610||17 Sep 1999||23 Oct 2001||Massachusetts Institute Of Technology||Biological applications of quantum dots|
|US6361944||25 Jun 1999||26 Mar 2002||Nanosphere, Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|US6365418||18 May 2000||2 Apr 2002||Zyomyx, Incorporated||Arrays of protein-capture agents and methods of use thereof|
|US6369206 *||19 Jul 2000||9 Apr 2002||Robert D. Leone||Metal organothiol particles|
|US6417340||20 Oct 2000||9 Jul 2002||Nanosphere, Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|US6720147 *||12 Oct 2001||13 Apr 2004||Nanosphere, Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|US20020172953||10 Aug 2001||21 Nov 2002||Mirkin Chad A.||Movement of biomolecule-coated nanoparticles in an electric field|
|US20030068622||12 Oct 2001||10 Apr 2003||Nanosphere, Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|US20030068638||2 Aug 2002||10 Apr 2003||William Cork||Nanoparticle imaging system and method|
|US20040101889||4 Aug 2003||27 May 2004||Northwestern University||Method of detection by enhancement of silver staining|
|EP0630974A2||21 Jun 1994||28 Dec 1994||Johnson & Johnson Clinical Diagnostics, Inc.||Method and test kit for the detection of inorganic orthophosphate by-product from amplification of target nucleic acid|
|EP0667398A2||2 Feb 1995||16 Aug 1995||Kyoto Dai-ichi Kagaku Co., Ltd.||Method of and apparatus for detecting specific base sequence of DNA|
|WO1989006801A1||11 Jan 1989||27 Jul 1989||Nycomed As||Test method and reagent kit therefor|
|WO1990002205A1||23 Aug 1989||8 Mar 1990||Angenics, Inc.||Detection of nucleic acid sequences using particle agglutination|
|WO1992004469A2||6 Sep 1991||19 Mar 1992||Imperial Chemical Industries Plc||Nucleic acid detection method using particle agglutination|
|WO1993010564A1||20 Nov 1992||27 May 1993||The Regents Of The University Of California||Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers|
|WO1993025709A1||9 Jun 1993||23 Dec 1993||Medical Research Council||Preparation of nucleic acids|
|WO1994029484A1||8 Jun 1994||22 Dec 1994||Gamera Bioscience Corporation||Magnetic cycle reaction|
|WO1997040181A1||17 Apr 1997||30 Oct 1997||Spectrametrix Inc.||Analyte assay using particulate labels|
|WO1998004740A1||21 Jul 1997||5 Feb 1998||Nanosphere Llc||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|WO1998010289A1||4 Sep 1997||12 Mar 1998||The Penn State Research Foundation||Self-assembled metal colloid monolayers|
|WO1998017317A2||21 Oct 1997||30 Apr 1998||Skw Trostberg Aktiengesellschaft||Process for producing biologically active polymer nanoparticle-nucleic acid conjugates|
|WO1999020789A1||16 Oct 1998||29 Apr 1999||Genicon Sciences Corporation||Analyte assay using particulate labels|
|WO1999021934A1||28 Oct 1998||6 May 1999||The University Of Melbourne||Stabilized particles and methods of preparation and use thereof|
|WO1999023258A1||30 Oct 1998||14 May 1999||Gen-Probe Incorporated||Methods of nucleic acid detection|
|WO1999060169A1||20 May 1999||25 Nov 1999||Molecular Machines, Inc.||Multimolecular devices, drug delivery systems and single-molecule selection|
|WO2000025136A1||27 Oct 1999||4 May 2000||Technion Research And Development Foundation Ltd.||Method for gold deposition|
|WO2000033079A1||30 Nov 1999||8 Jun 2000||Nanosphere, Inc.||Nanoparticles with polymer shells|
|WO2001000876A1||26 Jun 2000||4 Jan 2001||Mirkin Chad A||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|WO2001051665A2||12 Jan 2001||19 Jul 2001||Nanosphere Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|WO2001073123A2||28 Mar 2001||4 Oct 2001||Nanosphere Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|WO2001086301A1||10 May 2001||15 Nov 2001||Center For Advanced Science And Technology Incubation, Ltd.||Polymer composition for forming surface of biosensor|
|WO2002004681A2||11 Jul 2001||17 Jan 2002||Northwestern University||Method of detection by enhancement of silver staining|
|WO2002018643A2||10 Aug 2001||7 Mar 2002||Nanosphere Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|WO2002036169A2||31 Oct 2001||10 May 2002||Pr Pharmaceuticals, Inc.||Methods and compositions for enhanced delivery of bioactive molecules|
|WO2002046472A2||7 Dec 2001||13 Jun 2002||Nanosphere, Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|WO2002046483A2||30 Nov 2001||13 Jun 2002||Northwestern University||Silver stain removal from dna detection chips by cyanide etching or sonication|
|WO2004053105A2||12 Dec 2003||24 Jun 2004||Nanosphere, Inc.||Direct snp detection with unamplified dna|
|1||Ahmadi et al., "Shape-Controlled Synthesis of Colloidal Platinum Nanoparticles", Science, Jun. 28, 1996, vol. 272, pp. 1924-1926.|
|2||Alivisatos et al., "Organization of 'nanocrystal molecules' using DNA," Nature, vol. 382, pp. 609-611 (1996).|
|3||Bahnemann et al., "Mechanisms of Organic Transformations on Semiconductor Particles", Photochemical Conversion and Storage of Solar Energy, Proceedings of the Eighth International Conference on Photochemical Conversion and Storage of Solar Energy, IPS-8, held Jul. 15-20, 1990, in Palermo, Italy.|
|4||Bain, et al., "Modeling Organic Surfaces with Self-Assembled Monolayers," Angew. Chem. Int. Ed. Engl., vol. 28, pp. 506-512 (1989).|
|5||Bassell et al., "Single mRNAs Visualized by Ultrastructural In Situ Hybridization are Principally Localized at Actin Filament Intersections in Fibroblasts", The Journal of Cell Biology, Aug. 1994, vol. 126, No. 4, pp. 863-876.|
|6||Borman, Chem.Eng. News, Dec. 9, 1996, pp. 42-43 (1996).|
|7||Bottomley et al, "Scanning tunneling microscopy of DNA: The chemical modification of gold surfaces for immobilization of DNA", J. Vac. Sci. Technol. A, Jul./Aug. 1992, vol. 10, No. 4, pp. 591-595.|
|8||Brada, et al., "Golden Blot"-Detection of Polyclonal and Monoclonal Antibodies Bound to Antigens on Nitrocellulose by Protein A-Gold Complexes, Analytical Biochemistry, vol. 42, pp. 79-83 (1984) U.S.|
|9||Bradley, "The Chemistry of Transition Metal Colloids," Clusters and Colloids: From Theory to Applications, G. Schmid, Editor, BCH, Weinheim, New York, pp. 459-542 (1994).|
|10||Braun et al., "DNA-templated assembly and electrode attachment of a conducting silver wire", Nature, Feb. 19, 1998, vol. 391, pp. 775-778.|
|11||Braun-Howland et al., "Development of a Rapid Method for Detecting Bacterial Cells In Situ Using 16S rRNA-Targeted Probes", BioTechniques, 1992, vol. 13, No. 6, pp. 928-933.|
|12||Brus, "Quantum Crystallites and Nonlinear Optics", Applied Physics A, 1991, vol. 53 pp. 465-474.|
|13||Brust et al., "Novel Gold-Dithiol Nano-Networks with Non-Metallic Electronic Properties," Adv. Mater., vol. 7, pp. 795-797 (1995).|
|14||Caruthers et al., "Chemical Synthesis of Deoxyoligonucleotides by the Phosphoramidite Method," Methods in Enzymology, vol. 154, p. 287-313 (1987).|
|15||Chen & Seeman, "Synthesis from DNA of a molecule with the connectivity of a cube," Nature, vol. 350, pp. 631-633 (1991).|
|16||Chen et al., "A Specific Quadrilateral Synthesized from DNA Branched Junctions," J. Am. Chem. Soc., vol. 111, pp. 6402-6407 (1989).|
|17||Chen et al., Crystal Structure of a Four-Stranded Intercalated DNA: d(C<SUB>4</SUB>)<SUP>†‡ </SUP>Biochem., vol. 33, pp. 13540-13546 (1994).|
|18||Chrisey et al., "Covalent attachment of synthetic DNA to self-assembled monolayer films", Nucleic Acids Research, 1996, vol. 24, No. 15, pp. 3031-3039.|
|19||Chrisey et al., "Fabrication of patterned DNA surfaces", Nucleic Acids Research, 1996, vol. 24, No. 15, pp. 3040-3047.|
|20||Curtis et al., "A Morphology-Selective Copper Organosal", Angew. Chem. Int. Ed. Engl., 1988, vol. 27, No. 11, pp. 1530-1533.|
|21||Dagani, "Supramolecular Assemblies DNA to organize gold nanoparticles," Chemical & Engineering News, p. 6-7, Aug. 19, 1996.|
|22||Díaz et al., "Synthesis of Oligodeoxynucleotides Containing 2-Substituted Guanine Derivatives Using 2-Fluoro-2'-Deoxyinosine as Common Nucleoside Precursor", Nucleosides & Nucleotides, 1997, vol. 16, Nos. 10 & 11, pp. 2035-2051.|
|23||Dubois & Nuzzo, "Synthesis, Structure, and Properties of Model Organic Surfaces," Annu. Rev. Phys. Chem., vol. 43, pp. 437-464 (1992).|
|24||Dunn, et al., A Novel Method to Map Transcripts: Evidence for homology between an Adenovirus mRNA and Discrete Multiple Regions of the Viral Genome, Cell, vol. 12, pp. 23-36, (1997) U.S.|
|25||Elghanian et al., "Selective Colorimetric Detection of Polynucleotides Based on the Distance-Dependent Optical Properties of Gold Nanoparticles," Science, vol. 277, pp. 1078-1081 (1997).|
|26||Erlanson et al., "Disulfide Cross-linking as a Mechanistic Probe for the B-Z Transition of DNA", J. Am. Chem. Soc., 1997, vol. 119, pp. 6927-6928.|
|27||Goodwin et al., "Incorporation of Alkyithiol Chains at C-5 of Deoxyuridine", Tetrahedron Letters, 1993, vol. 34, No. 35, pp. 5549-5552.|
|28||Grabar et al., "Preparation and Characterization of Au Colloid Monolayers," Anal. Chem. vol. 67, pp. 735-743 (1995).|
|29||Hacia et al., "Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis," Nature Genet., vol. 14, pp. 441-447 (1996).|
|30||Hacker, High performance Nanogold-Silver in situ hybridisation, Eur. J. Histochem, vol. 42, pp. 111-120 (1998) U.S.|
|31||Hegner et al., "Immobilizing DNA on gold via thiol modification for atomic force microscopy imaging in buffer solutions", FEBS, Dec. 1993, vol. 336, No. 3, pp. 452-456.|
|32||Henglein, "Absorption Spectrum and Some Chemical Reactions of Colloidal Platinum in Aqueous Solution", J. Phys. Chem., 1995, vol. 99, pp. 14129-14136.|
|33||Henglein, "Mechanism of Reactions on Colloidal Microelectrodes and Size Quantization Effects", Topics in Current Chemistry, 1988, vol. 143, pp. 113-180.|
|34||Henglein, "Small-particle Research: Physicochemical Properties of Extremely Small Colloidal Metal and Semiconductor Particles", Chem. Rev., 1989, vol. 89, pp. 1861-1873.|
|35||Jacoby, "Nanoparticles change color on binding to nucleotide target," Chemical &Engineering News, p. 10, Aug. 25, 1997.|
|36||Letsinger et al., "Control of Excimer Emission and Photochemistry of Stilbene Units by Oligonucleotide Hybridization," J. Am. Chem. Soc., vol. 116, pp. 811-812 (1994).|
|37||Letsinger et al., "Tailored Hydrophbic Cavitites of Oligonucleotide-Steroid Conjugates," Bioconjugate Chem., vol. 9, p. 826-830 (1998).|
|38||Letsinger et al., Use of Hydrophobic Substituents in Controlling Self-Assembly of Oligonucleotides, J. Am. Chem. Soc., vol. 115, pp. 7535-7536 (1993).|
|39||Letsinger, R., et al., "Chemistry of Oligonucleotide-Gold Nanoparticle Conjugates," Phosphorus, Sulfur and Silicon, vol. 144, p. 359-362 (1999).|
|40||Letsinger, R., et al., "Use of a Steroid Cyclic Disulfide Anchor in Constructing Gold Nanoparticle-Oligonucleotide Conjugates," Bioconjugate Chem, p. 289-291 (2000).|
|41||Li Z., et al., "Multiple thiol-anchor capped DNA-gold nanoparticle conjugates," Nucleic Acids Research, vol. 30, p. 1558-1562 (2002).|
|42||Mansfield et al., "Nucleic acid detection using non-radioactive labeling methods", Molecular and Cellular Probes, 1995, vol. 9, pp. 145-156.|
|43||Marsh et al., "A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy," Nucleic Acids Res., vol. 23, pp. 696-700 (1995).|
|44||Massart, "Preparation of Aqueous Magnetic Liquids in Alkaline and Acidic Media", IEEE Transactions on Magnetics, Mar. 1981, vol. MAG-17, No. 2, pp. 1247-1248.|
|45||Mirkin et al., "A DNA-based method for rationally assembling nanoparticles into macroscopic materials," Nature, vol. 382, pp. 607-609 (1996).|
|46||Mirkin et al., "DNA-Induced Assembly of Gold Nanoparticles: A Method for Rationally Organizing Colloidal Particles into Ordered Macroscopic Materials," Abstract 249, Abstracts of Papers Part 1, 212 ACS National Meeting 0-8412-3402-7, American Chemical Society, Orlando, FL, Aug. 25-29, 1996.|
|47||Mirkin, "H-DNA and Related Structures," Annu. Review Biophys. Biomol. Struct., vol. 23, pp. 541-576 (1994).|
|48||Mohanty J., et al. "Pulsed laser excitation of phosphate stabilized silver nanoparticles," Proc. Indian Acd. Sci., vol. 112, No. 1, p. 63-72.|
|49||Mucic et al., "Synthesis and characterization of DNA with ferrocenyl groups attached to their 5'-termini: electrochemical characterization of a redox-active nucleotide monolayer", Chemical Communications, 1996, pp. 555-557.|
|50||Mucic et al., "Synthesis and characterizations of DNA with ferrocenyl groups attached to their 5'-termini: electrochemical characterization of a redox-active nucleotide monolayer," Chem. Commun., pp. 555-557 (1996).|
|51||Mulvaney, "Surface Plasmon Spectroscopy of Nanosized Metal Particles," Langmuir, vol. 12, pp. 788-800 (1996).|
|52||Nechev et al., "Stereospecific Synthesis of Oligonucleotides Containing Crotonaldehyde Adducts of Deoxyguanosine", Chem. Res. Toxicol., 2001, vol. 14, pp. 1506-1512.|
|53||Nicewarmer- Pena S., et al., "Hybridization and Enzymatic Extension of Au Nanoparticle-Bound Oligonucleotides," J. Am. Chem. Soc., vol. 124, p. 7314-7323 (2002).|
|54||Nuzzo R., et al., "Spontaneously Organized Molecular Assemblies. 3. Preparation and Properties of Solution Adsorbed Monolayers of Organic Disulfides on Gold Surfaces," J. Am. Chem. Soc., vol. 109, p. 2358-2368 (1987).|
|55||O.D. Velev, et al., "In Situ Assembly of Collordal Particles into Miniaturized Biosensors," Langmuir, vol. 15, No. 11, pp. 3693-3698, May 25, 1999.|
|56||Otsuka, H., et al., "Quantitative and Reversible Lectin-Induced Association of Gold Nonoparticles Modified with alpha-Lactosyl-omega-mercapto-poly(ethyleneglycol)," J. Am. Chem. Soc., vol. 123, p. 8226-8230 (2001).|
|57||Pierce, 2-Iminothiolane.HC1 (Traut's Reagent), No. 26101, p. 1-3.|
|58||Rabke-Clemmer et al., "Analysis of Functionalized DNA Adsorption on Au(111) Using Electron Spectroscopy," Langmuir, vol. 10, pp. 1796-1800 (1994).|
|59||Ranki, et al., "Sandwich hybridization as a convenient method for the detection of nucleic acids in crude samples," Gene, vol. 21, pp. 77-85 (1983) U.S.|
|60||Romano, et al., "An antiglobulin reagent labelled with colloidal gold for use in electron microscopy," Immunochemistry, vol. 11, pp. 521-522 (1974) Great Britain.|
|61||Roubi, "Molecular Machines-Nanodevice with rotating arms assembled from synthetic DNA," Chemical & Engineering News, p. 13, (Jan. 1999).|
|62||Seeman et al., "Synthetic DNA knots and catenanes," New J Chem., vol. 17, pp. 739-755 (1993).|
|63||Shaw & Wang, "Knotting of a DNA Chain During Ring Closure," Science, vol. 260, pp. 533-536 (1993).|
|64||Shekhtman et al., "Sterostructure of replicative DNA catenanes from eukaryotic cells," New J. Chem. vol. 17, pp. 757-763 (1993).|
|65||Smith and Feigon, "Quadruplex structure of Oxytricha telomeric DNA oligonucleotides," Nature, vol. 356, pp. 164-168 (1992).|
|66||Stimpson, et al., "Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides," Proc. Natl. Acad. Sci.., vol. 92, pp. 6379-6383, California Institute of Technology (1995) U.S.|
|67||Storhoff, et al., "One-Pot Colorimetric Differentiation of Polynucleotides with Single Base Imperfections Using Gold Nanparticle Probes," J. Am. Chem. Soc., vol. 20, pp. 1961-1964, American Chemical Society (1998) U.S.|
|68||Storhoff, et al., "Strategies for Organizing Nanoparticles into Aggregate Structures and Functional Materials," Journal of Cluster Science, vol. 8, No. 2, pp. 179-217, Plenum Publishing Corporation (1997) U.S.|
|69||TechNote #205 Rev. #002, Section V. Coupling Protocols, Heading A. Carboxyl-Modified Microspheres, pp. 4 and 5 (Aug. 31, 1999).|
|70||Thein et al., "The use of synthetic oligonucleotides as specific hybridization probes in the diagnosis of genetic disorders," 2<SUP>nd </SUP>Ed., K.E. Davies, Ed., Oxford University Press, Oxford, New York, Tokyo, p. 21-33 (1993).|
|71||Tomlinson et al., Anal. Biochem, vol. 171, pp. 217-222 (1998).|
|72||Uchida et al., "GaAs Nanocrystals Prepared in Quinoline", J. Phys Chem., 1991, vol. 95, pp. 5382-5384.|
|73||Velev, et al., "In Situ Assembly of Colloidal Particles into Miniaturized Biosensors," Langmuir, vol. 15, No. 11, pp. 3693-3698, American Chemical Society (1999) U.S.|
|74||Wang et al., "A DNA Aptamer Which Binds to and Inhibits Thrombin Exhibits a New Structural Motif for DNA," Biochem., vol. 32, pp. 1899-1904 (1993).|
|75||Wang et al., "Assembly and Characterization of Five-Arm and Six-Arm DNA Brached Junctions," Biochem., vol. 30, pp. 5667-5674 (1991).|
|76||Wang et al., "Nanometer-Sized Semiconductor Clusters: Materials Synthesis, Quantum Size Effects, and Photophysical Properties", J. Phys. Chem., 1991, vol. 95, pp. 525-532.|
|77||Weisbecker et al., "Molecular Self-Assembly of Aliphatic Thiols on Gold Colloids," Langmuir, vol. 12, pp. 3763-3772 (1996).|
|78||Weller, "Colloidal Semiconductor Q-Particles: Chemistry in the Transition Region Between Solid State and Molecules", Angew. Chem. Int. Engl., 1993, vol. 32, pp. 41-53.|
|79||Wells, "Unusual DNA Structures," J. Biol. Chem., vol. 263, pp. 1095-1098 (1988).|
|80||Whitesides G.M., et al., "Soft Lithography in Biology and Biochemistry," Annu. Rev. Biomed. Eng., p. 335-373 (2001).|
|81||Wuelfing, P., et al., "Nanometer Gold Clusters Protected by Surface-Bound Monolayers of Thiolated Poly(ethylene glycol) Polymer Electrolyte," J. Am. Chem. Soc., vol. 120, p. 12696-12697 (1998).|
|82||Yguerabide, et al., "Light-Scattering Submicroscopic Particles as Highly Fluorescent Analogs and Their Use as Tracer Labels in Clinical and Biological Applications," I. Theory, Analytical Biochemistry, vol. 262, pp. 137-156 (1998) U.S.|
|83||Yguerabide, et al., "Light-Scattering Submicroscopic Particles as Highly Fluorescent Analogs and Their Use as Tracer Labels in Clinical and Biological Applications," II. Experimental Characterization, Analytical Biochemistry, vol. 262, pp. 157-176 (1998) U.S.|
|84||Zammatteo, et al., "Comparison between Different Strategies of Covalent Attachment of DNA to Glass Surfaces to Build DNA Microarrays," Analytical Biochem., vol. 280, 143-150 (2000).|
|85||Zhang et al., "Informational Liposomes: Complexes Derived from Cholesteryl-conjugated Oligonucleotides and Liposomes," Tetrahedron Lett., vol. 37, pp. 6243-6246 (1996).|
|86||Zhu, et al., "The First Raman Spectrum of an Organic Monolayer on a High-Temperature Superconductor: Direct Spectroscopic Evidence for a Chemical Interaction between an Amine and Yba<SUB>2</SUB>Cu<SUB>3</SUB>O<SUB>7-delta</SUB>," J. Am. Chem. Soc., vol. 119, pp. 235-236, American Chemical Society (1997) U.S.|
|87||Zimmermann et al., "DNA stretching on functionalized gold surfaces", Nucleic Acids Research, 1994, vol. 22, No. 3, pp. 492-497.|
|Citing Patent||Filing date||Publication date||Applicant||Title|
|US8323888||2 Feb 2007||4 Dec 2012||Nanosphere, Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|US8604184 *||5 May 2010||10 Dec 2013||The United States Of America As Represented By The Secretary Of The Air Force||Chemically programmable immunity|
|US8946389 *||25 Apr 2012||3 Feb 2015||University Of Washington||Compositions and methods for multiplex biomarker profiling|
|US9376717||19 Dec 2014||28 Jun 2016||University Of Washington Through Its Center For Commercialization||Compositions and methods for multiplex biomarker profiling|
|US9512468||6 Nov 2012||6 Dec 2016||Industrial Technology Research Institute||Detection method uses magnetic and detectable nanoparticles with oligonucleotides attached thereto|
|US20030096321 *||1 Jul 2002||22 May 2003||Jose Remacle||Method for the identification and/or the quantification of a target compound obtained from a biological sample upon chips|
|US20060134694 *||22 Dec 2004||22 Jun 2006||Intel Corporation||Methods of protein profiling by thiolation|
|US20060177852 *||4 Jan 2006||10 Aug 2006||Do-Coop Technologies Ltd.||Solid-fluid composition|
|US20090004296 *||4 Jan 2007||1 Jan 2009||Do-Coop Technologies Ltd.||Antiseptic Compositions and Methods of Using Same|
|US20090029340 *||4 Jan 2007||29 Jan 2009||Do-Coop Technologies Ltd.||Cryoprotective Compositions and Methods of Using Same|
|US20090185113 *||23 Apr 2008||23 Jul 2009||Industrial Technology Research Institute||Color Filter Module and Device of Having the Same|
|US20090253613 *||4 Jan 2007||8 Oct 2009||Do-Coop Technologies Ltd.||Solid-Fluid Composition|
|US20090325812 *||2 Feb 2007||31 Dec 2009||Nanosphere, Inc.||Nanoparticles having oligonucleotides attached thereto and uses therefor|
|US20100041103 *||3 Jan 2008||18 Feb 2010||Do-Coop Technologies Ltd.||Composition and method for enhancing cell growth and cell fusion|
|US20100086929 *||3 Jan 2008||8 Apr 2010||Do-Coop Technologies Ltd.||Detection of analytes|
|US20100113301 *||1 Dec 2009||6 May 2010||Eppendorf Array Technologies||Method for the identification and/or the quantification of a target compound obtained from a biological sample upon chips|
|US20100267007 *||8 Jan 2009||21 Oct 2010||Do-Coop Technologies Ltd.||Solid-fluid composition and uses thereof|
|US20100285052 *||5 May 2010||11 Nov 2010||Mullis Kary B||Chemically Programmable Immunity|
|US20100291541 *||14 May 2009||18 Nov 2010||Evoy Stephane||Bacteriophage immobilization for biosensors|
|US20150004598 *||25 Apr 2012||1 Jan 2015||University Of Washington||Compositions and methods for multiplex biomarker profiling|
|EP2614834A1||7 Mar 2008||17 Jul 2013||UTI Limited Partnership||Compositions and methods for the prevention and treatment of autoimmune conditions|
|EP2842570A1||7 Mar 2008||4 Mar 2015||Uti Limited Partnership||Compositions and methods for the prevention and treatment of autoimmune conditions|
|WO2012041968A1||29 Sep 2011||5 Apr 2012||Uti Limited Partnership||Methods for treating autoimmune disease using biocompatible bioabsorbable nanospheres|
|WO2012062904A2||11 Nov 2011||18 May 2012||Uti Limited Partnership||Compositions and methods for the prevention and treatment of cancer|
|U.S. Classification||536/23.1, 536/24.3, 536/25.3, 435/6.11|
|International Classification||G01N33/566, G01N33/532, C12Q1/68, C12N15/09, G01N33/553, C07H21/02, G01N33/58, C07H21/04, C07H21/00, G01N33/543|
|Cooperative Classification||G01N33/54306, G01N33/587, C07H21/00|
|European Classification||C07H21/00, G01N33/543B, G01N33/58H4|
|25 Feb 2003||AS||Assignment|
Owner name: NANOSPHERE, INC., ILLINOIS
Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:GARIMELLA, VISWANADHAM;STORHOFF, JAMES J.;REEL/FRAME:013777/0870;SIGNING DATES FROM 20020205 TO 20030206
|24 Apr 2007||AS||Assignment|
Owner name: VENTURE LENDING & LEASING IV, INC., CALIFORNIA
Free format text: SECURITY INTEREST;ASSIGNOR:NANOSPHERE, INC.;REEL/FRAME:019227/0165
Effective date: 20070221
Owner name: VENTURE LENDING & LEASING V, INC., CALIFORNIA
Free format text: SECURITY INTEREST;ASSIGNOR:NANOSPHERE, INC.;REEL/FRAME:019227/0165
Effective date: 20070221
Owner name: VENTURE LENDING & LEASING IV, INC.,CALIFORNIA
Free format text: SECURITY INTEREST;ASSIGNOR:NANOSPHERE, INC.;REEL/FRAME:019227/0165
Effective date: 20070221
Owner name: VENTURE LENDING & LEASING V, INC.,CALIFORNIA
Free format text: SECURITY INTEREST;ASSIGNOR:NANOSPHERE, INC.;REEL/FRAME:019227/0165
Effective date: 20070221
|11 Oct 2010||REMI||Maintenance fee reminder mailed|
|6 Mar 2011||REIN||Reinstatement after maintenance fee payment confirmed|
|6 Mar 2011||LAPS||Lapse for failure to pay maintenance fees|
|26 Apr 2011||FP||Expired due to failure to pay maintenance fee|
Effective date: 20110306
|13 Jun 2011||PRDP||Patent reinstated due to the acceptance of a late maintenance fee|
Effective date: 20110617
|17 Jun 2011||SULP||Surcharge for late payment|
|17 Jun 2011||FPAY||Fee payment|
Year of fee payment: 4
|9 Apr 2013||AS||Assignment|
Owner name: NANOSPHERE, INC., ILLINOIS
Free format text: RELEASE BY SECURED PARTY;ASSIGNORS:VENTURE LENDING & LEASING IV, INC.;VENTURE LENDING & LEASING V, INC.;REEL/FRAME:030182/0433
Effective date: 20130408
|6 Aug 2014||FPAY||Fee payment|
Year of fee payment: 8
|16 Jun 2015||AS||Assignment|
Owner name: NSPH FUNDING LLC, DELAWARE
Free format text: SECURITY INTEREST;ASSIGNOR:NANOSPHERE, INC.;REEL/FRAME:035921/0289
Effective date: 20150514
|12 Jul 2016||AS||Assignment|
Owner name: NANOSPHERE, INC., ILLINOIS
Free format text: RELEASE BY SECURED PARTY;ASSIGNOR:NSPH FUNDING LLC;REEL/FRAME:039313/0919
Effective date: 20160630